Filters
Technology
Platform
GSE141170
Homo sapiens
4 Downloadable Samples
Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
Macophage migration inhibitor (MIF) is important for MM resistance to proteasome inhibitors. To determine what signalling pathways are affected by MIF in MM cells, we established MIF-KO MM.1S and ARP-1 MM cell lines. Total RNAs of 2 x 106 CTR-KO and MIF-KO MM cells were extracted by RNeasy Mini Kit (Qiagen). 5-10 µg RNA samples were sent to Gene Expression and Genotyping Facility at Case Western Reserve University (Cleveland, OH) for RNA-seq followed by data analysis.
Publication Title
MIF as a biomarker and therapeutic target for overcoming resistance to proteasome inhibitors in human myeloma.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Rattus norvegicus
- 15 Downloadable Samples
- Affymetrix Rat Gene 2.1 ST Array (ragene21st)
Description
Analysis of the effects of sulphatide specific antibody (O4, 20microg/ml) on myelinating cultures generated from dissociated embryonic rat spinal cord after 24 hours treatment to give insights into effects of lipid-specific antibodies and its implication in demyelinating diseases.
Publication Title
Lipid-specific IgMs induce antiviral responses in the CNS: implications for progressive multifocal leukoencephalopathy in multiple sclerosis.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Klinefelters Syndrome (KS) is one of the common chromosome aneuploidy diseases in males with unexplained physiological mechanism. iPSCs, are similar to ESCs in terms of indefinitive self-renewal and pluripotency, provided an alternative choice for modeling disease to facilitate the disease research in vitro.
Publication Title
Aberrant gene expression profiles in pluripotent stem cells induced from fibroblasts of a Klinefelter syndrome patient.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Gene 2.0 ST Array (ragene20st)
Description
Diabetic rats changes gene exprssion in liraglutide treated rats cardiac muscle
Publication Title
Liraglutide protects cardiac function in diabetic rats through the PPARα pathway.
Sample Metadata Fields
Age, Specimen part
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Gene 2.0 ST Array (ragene20st)
Description
More and more evidence shows that maternal overnutrition may increase the risk of diabetes in offspring. This study aimed to find out whether maternal early sitagliptin intervention improves glucose intolerance through gut target in offspring.
Publication Title
Maternal sitagliptin treatment attenuates offspring glucose metabolism and intestinal proinflammatory cytokines IL-6 and TNF-α expression in male rats.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 18 Downloadable Samples
IlluminaHiSeq2000
Description
Alu elements are major contributors to lineage-specific new exons in primate and human genomes. Recent studies indicate that some Alu exons have high transcript inclusion levels or tissue-specific splicing profiles, and may play important regulatory roles in modulating mRNA degradation or translational efficiency. However, the contribution of Alu exons to the human proteome remains unclear and controversial. The prevailing view is that exons derived from young repetitive elements, such as Alu elements, are restricted to regulatory functions and have not had adequate evolutionary time to be incorporated into stable, functional proteins. We adopt a proteotranscriptomics approach to systematically assess the contribution of Alu exons to the human proteome. Using RNA sequencing, ribosome profiling and proteomics data from human tissues and cell lines, we provide evidence for the translational activities of Alu exons and the presence of Alu exon derived peptides in human proteins. These Alu exon peptides represent species-specific protein differences between primates and other mammals, and in certain instances between humans and closely related primates. In the case of the RNA editing enzyme ADARB1, which contains an Alu exon peptide in its catalytic domain, RNA sequencing analyses of A-to-I editing demonstrate that both the Alu exon skipping and inclusion isoforms encode active enzymes. The Alu exon derived peptide may fine tune the overall editing activity and, in limited cases, the site selectivity of ADARB1 protein products. Our data indicate that Alu elements have contributed to the acquisition of novel protein sequences during primate and human evolution. Overall design: Comparing the A-I RNA editing levels of HEK293 cells transfected with empty vector (CV) control, Alu exon inclusion (long) isoform of ADARB1, and Alu exon skipping (short) isoform of ADARB1. Each group has 3 replicates.
Publication Title
The contribution of Alu exons to the human proteome.
Sample Metadata Fields
No sample metadata fields
View Samples- Escherichia coli
- 6 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Glyphosate (GLY) is an effective antimetabolite that acts against the shikimate pathway 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, However, little is known about the genome-scale transcriptional responses of bacteria after glyphosate shock. To investigate further the mechanisms by which E. coli response to a glyphosate shock, a DNA-based microarray was used for transcriptional analysis of E. coli exposed to 200 mM glyphosate.
Publication Title
Genome-wide transcriptional responses of Escherichia coli to glyphosate, a potent inhibitor of the shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase.
Sample Metadata Fields
Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 4000
Description
Induced pluripotent stem cells (iPSCs) can be derived from somatic cells through ectopic expression of transcriptional factors or chemical cocktails. Chemical reprogramming might be safe than transcriptional factors since there is no integration of exogenous genes. However, there is still little direct evidence to prove this hypothesis. In this study, we have performed whole genome profiling of the DNA methylomes of mouse chemical iPSCs (CiPSCs), transcriptional factors induced iPSCs (TF-iPSCs) and embryonic stem cells (ESCs). We find that the methylation levels of high-CpG-density promoters (HCPs) and intermediate- CpG-density promoters (ICPs) have no significant difference among them, but low-CpG-density promoters (LCP) and three retrotransposons (LINEs, LTRs and SINEs) show preference to different methylation levels. Surprisingly, CiPSCs are hypomethylated than TF-iPSCs and the major difference of methylation levels lies in the intergenic regions while two iPSCs lines are generally hypermethylated compared to ESCs. Moveover, we find the methylation states of imprinting control regions (ICRs) and the expression of imprinted genes of CiPSCs are more resemble ESCs than TF-iPSCs. Our data first provide the epigenetic states of chemical induced pluripotent stem cells and compare the difference of mouse CiPSCs, TF-iPSCs and ESCs. These observations might affect ongoing choices of reprogramming methods for disease modeling and give some guides for potential therapeutic applications. Overall design: Comparison of DNA methylation and genes expression patterns in 3 cell types
Publication Title
Genome-wide DNA methylation analysis reveals that mouse chemical iPSCs have closer epigenetic features to mESCs than OSKM-integrated iPSCs.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To exploit targets or signaling pathways affected by PLS-123 during anti-tumor process, gene expression profiling was carried out in representative OCI-Ly7 cells treated for 24 hours.
Publication Title
Irreversible dual inhibitory mode: the novel Btk inhibitor PLS-123 demonstrates promising anti-tumor activity in human B-cell lymphoma.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
To exploit targets or signaling pathways affected by PLS-123 during anti-tumor process, gene expression profiling was carried out in OCI-Ly7 inoculated xenograft model.
Publication Title
Irreversible dual inhibitory mode: the novel Btk inhibitor PLS-123 demonstrates promising anti-tumor activity in human B-cell lymphoma.
Sample Metadata Fields
Specimen part
View Samples